Introduction to Bioimage Analysis using QuPath

This deck of slides introduces participants to the main ideas of bioimage analysis using the open-source software QuPath. It is designed as a primer on QuPath for busy biologists who need to analyze images part of their research.

These materials were initially designed for a workshop taught in-person at Harvard Medical School - organized by the Image Analysis Collaboratory.

Download the course materials:

1. Slides: Download PDF

Contents

• Introduction to image analysis
• Introduction to QuPath
• QuPath projects and user-interface
• Cell detection and measurements
• Cell classification
• Tissue annotation and spatial measurements
• Scripting, workflows and batch processing